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Volunteer patients were randomized into one of two experiment groups where they would receive an experimental vaccine or a placebo. They were subsequently exposed to a drug-sensitive strain of malaria and observed to see whether they came down with an infection.




A data frame with 20 observations on the following 2 variables.


Whether a person was given the experimental vaccine or a placebo.


Whether the person got an infection or no infection.


Lyke et al. 2017. PfSPZ vaccine induces strain-transcending T cells and durable protection against heterologous controlled human malaria infection. PNAS 114(10):2711-2716. doi: 10.1073/pnas.1615324114 .


In this study, volunteer patients were randomized into one of two experiment groups: 14 patients received an experimental vaccine or 6 patients received a placebo vaccine. Nineteen weeks later, all 20 patients were exposed to a drug-sensitive malaria virus strain; the motivation of using a drug-sensitive strain of virus here is for ethical considerations, allowing any infections to be treated effectively.



# Calculate conditional probabilities of infection after vaccine/placebo
malaria %>%
  count(treatment, outcome) %>%
  group_by(treatment) %>%
  mutate(prop = n / sum(n))
#> # A tibble: 3 × 4
#> # Groups:   treatment [2]
#>   treatment outcome          n  prop
#>   <fct>     <fct>        <int> <dbl>
#> 1 placebo   infection        6 1    
#> 2 vaccine   infection        5 0.357
#> 3 vaccine   no infection     9 0.643

# Fisher's exact text
#> 	Fisher's Exact Test for Count Data
#> data:  table(malaria)
#> p-value = 0.01409
#> alternative hypothesis: true odds ratio is not equal to 1
#> 95 percent confidence interval:
#>  1.338381      Inf
#> sample estimates:
#> odds ratio 
#>        Inf